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gb_harvester_chunk.sh
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gb_harvester_chunk.sh
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#!/bin/sh
# Calling sequence
# $ qsub -v cfgfile=/path/to/config.yaml /path/to/script.R
## set name of script
#PBS -N ben-gb_harvester
## send the environment variables
#PBS -V
#PBS -q route
#PBS -l walltime=384:00:00
#PBS -l select=1:ncpus=4:mem=128GB
# log options (in addition to logging by script)
#PBS -e /mnt/storage/data/edna/mednaTaxaRef/egrey
#PBS -o /mnt/storage/data/edna/mednaTaxaRef/egrey
# mail options
#PBS -m bea
#PBS -M btupper@bigelow.org
## access resources
module use /mod/bigelow
module load R
CODEPATH=$(head -n 1 ~/.referee)
cd $CODEPATH
Rscript ${CODEPATH}/gb_harvester_chunk.R ${cfgfile}